text: //usage covermax -n to-mutate -c coverage filename.fasta
  #include <stdlib.h>
  #include <stdio.h>
  #include <sys/types.h>
  #include <dirent.h>
  #include <string.h>
  #include <time.h>
  #include "covermax.h"
  
  
  int main (int argc, char **argv)
  {
      srand(time(NULL)); //seed prng
      int coverage=0, tomutate=0;
      if (argc > 5)
      {
          for (int i=1; i<4; i++)
          {
              if (strstr(argv[i], "-n") != NULL)
              {
                  if (strchr(argv[i+1], '*') != NULL)
                  {
                      tomutate=-1;
                      //printf("set mutate = %d\n", tomutate);
                  }
                  else
                  {
                      tomutate=atoi(argv[i+1]);
                      //printf("set mutate = %d\n", tomutate);
                  }
              }
              if (strstr(argv[i], "-c") != NULL)
              {
                  coverage=atoi(argv[i+1]);
                 // printf("coverage = %d\n", coverage);
              }
          }
          //FILE *filepoint=fopen("test.fasta", "r+");
          FILE *filepoint=fopen(argv[5], "r");
          if (filepoint == NULL)
          {
              printf("Could not open file, exiting now.\n");
          }
          char *read=malloc(sizeof(char)*3000), *header=malloc(sizeof(char)*100);
          if (coverage <= -1)
          {
              while (!feof(filepoint))
              {
                //  printf("cont mutating: %s\n", header);
                  get_fasta_chunk(filepoint, &header, &read, 100, 3000);
                  amplify(&read, strlen(read), coverage);
              }
          }
          else
          {
              //printf("to mutate= %d coverage = %d\n", tomutate, coverage);
              for (int i=0; i<tomutate; i++)
              {
                  get_fasta_chunk(filepoint, &header, &read, 100, 3000);
                  printf("mutating: %s\n", header);
                  amplify(&read, strlen(read), coverage);
              }
          }
         // get_fasta_chunk(filepoint, &header, &read, 100, 3000);
          // printf("obtained header: %s\nobtained data: %s\n", header, read);
          // printf("obtained header: %s\nobtained data: %s\n", header2, read2);
         // printf("mutating: %s\n", header);
         // amplify(&read, strlen(read), 30);
      }
      else
      {
          printf("COVERMAX\nUsage: covermax -c <coverage> -n <number-of-fastas-to-mutate> <input-file>\n");
      }
      return 0;
  }
  